BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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BMRB Entry 34056

Title: Structure of DNA AGCGA-quadruplex adopted by 15-mer oligonucleotide found in regulatory region of the PLEKHG3 human gene with G11 to I11 mutation, d(GCGAGGGAGCIAGGG),VK34_I11   PubMed: 28513602

Authors: Kocman, V.; Plavec, J.

Citation: Kocman, V.; Plavec, J.. "Tetrahelical structural family adopted by AGCGA-rich regulatory DNA regions."  Nat. Commun. 8, 15355-15355 (2017).

Assembly members:
entity_1, polymer, 15 residues, 4750.071 Da.

Natural source:   Common Name: Human   Taxonomy ID: 9606   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Homo sapiens

Experimental source:   Production method: chemical synthesis

Entity Sequences (FASTA):
entity_1: GCGAGGGAGCXAGGG

Data sets:
Data typeCount
1H chemical shifts79

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_1, 11
2entity_1, 21

Entities:

Entity 1, entity_1, 1 15 residues - 4750.071 Da.

1   DGDCDGDADGDGDGDADGDC
2   DIDADGDGDG

Samples:

sample_1: DNA (5'-D(*GP*CP*GP*AP*GP*GP*GP*AP*GP*CP*IP*AP*GP*GP*G)-3') 1 mM; LiCl 100 mM

sample_2: DNA (5'-D(*GP*CP*GP*AP*GP*GP*GP*AP*GP*CP*IP*AP*GP*GP*G)-3'), residue specific 15N labeled, 1 mM; LiCl 100 mM

sample_conditions_1: ionic strength: 100 mM; pH: 6; pressure: 1 atm; temperature: 273 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
1D 1H-15N HSQCsample_2isotropicsample_conditions_1
2D 1H-15N HSQCsample_2isotropicsample_conditions_1

Software:

AMBER, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement, structure calculation

SPARKY, Goddard - chemical shift assignment, peak picking

NMR spectrometers:

  • Agilent-Varian Uniform NMR System 600 MHz
  • Agilent-Varian Uniform NMR System 800 MHz

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